Rapid and comprehensive identification of prokaryotic organisms

Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Preparing compound containing saccharide radical

Reexamination Certificate

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Reexamination Certificate

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08076104

ABSTRACT:
An improved method for rapid identification of microorganisms is disclosed, along with sequences of PCR primers optimized for this purpose. The primers are designed based on information analysis of sequences from a large number of organism to amplify certain segments of genomic DNA whose sequences are unique among different organisms. The PCR products are compared with a DNA sequence database to obtain the identity of the microorganisms. This approach provides an accurate and fast identification and taxonomic assignment of microbial species.

REFERENCES:
patent: 5426027 (1995-06-01), Lott et al.
patent: 5547835 (1996-08-01), Koster
patent: 5622824 (1997-04-01), Koster
patent: 5691141 (1997-11-01), Koster
patent: 5849492 (1998-12-01), Rogan
patent: 5851765 (1998-12-01), Koster
patent: 5872003 (1999-02-01), Koster
patent: 6074823 (2000-06-01), Koster
patent: 6140053 (2000-10-01), Koster
patent: 6194144 (2001-02-01), Koster
patent: 6225450 (2001-05-01), Koster
patent: 6238871 (2001-05-01), Koster
patent: 6268131 (2001-07-01), Kang et al.
patent: 7108974 (2006-09-01), Ecker et al.
patent: 7217510 (2007-05-01), Ecker et al.
patent: 7226739 (2007-06-01), Ecker et al.
patent: 7255992 (2007-08-01), Ecker et al.
patent: 2004/0161770 (2004-08-01), Ecker et al.
patent: 2004/0209260 (2004-10-01), Ecker et al.
patent: 2004/0219517 (2004-11-01), Ecker et al.
patent: 2005/0130196 (2005-06-01), Hofstadler
patent: 2005/0164215 (2005-07-01), Hofstadler
patent: 2005/0266397 (2005-12-01), Ecker et al.
patent: 2005/0270191 (2005-12-01), Hofstadler
patent: 2006/0121520 (2006-06-01), Ecker et al.
patent: 2006/0205040 (2006-09-01), Sampath et al.
patent: 2006/0240412 (2006-10-01), Hall
patent: 2006/0259249 (2006-11-01), Sampath et al.
patent: 2006/0275749 (2006-12-01), Sampath et al.
patent: 2006/0275788 (2006-12-01), Ecker et al.
patent: 2007/0264639 (2007-11-01), Zenser et al.
patent: 2009/0280471 (2009-11-01), Ecker et al.
Li et al., Journal of Virological Methods, vol. 142, pp. 218-222, 2007.
Baldwin et al. Nuclear rDNA Evidence for Major Lineages of Helenioid Heliantheae (Compositae); Systematic Botany, 2002, vol. 27(1). p. 161-198.
Schilling, E.E., et al. A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae). I. Basal lineages, Botanical Journal of the Linnean Society, 2002, vol. 140, pp. 65-76.
Lowe T., et al., A computer program for selection of oligonucleotide primers for polymerase chain reactions, Nucleic acid research, 1990, vol. 18(7), pp. 1757-1761.
U.S. Appl. No. 12/058,353, Office Action dated Oct. 7, 2009, 13 pages.
U.S. Appl. No. 12/058,353, Search Reports cited in Office Action dated Oct. 7, 2009, 13 pages.
U.S. Appl. No. 12/058,353, Response to Office Action filed Feb. 8, 2010, 13 pages.
Aceto, S., et al.; Phylogeny and evolution of Orchis and allied genera based on ITS DNA variation: morphological gaps and molecular continuity; Mol Phylogenet Evol., Oct. 1999;13(1); pp. 67-76.
Ainouche, M.L. & Bayer, R.J. “On the origins of the tetraploid Bromus species (section Bromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA” Genome, Oct. 1997; 40(5); pp. 730-743.
Bains, W. “DNA Sequencing by Mass Spectrometry. Outline of a Potential Future Application” Chimicaoggi. vol. 9, No. 10, Oct. 1991; pp. 13-16, 1991.
Binns, S.E., et al. “A taxonomic revision ofEchinacea(Asteraceae: Heliantheae)” Syst. Bot. 2002, vol. 27, pp. 610-632.
Bobowski, B.R., et al. “Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis” Mol Ecol. Mar. 1999; 8(3); pp. 485-491.
Chen, C.H. Winston, et al.; Laser Desorption Mass Spectrometry for Fast DNA Sequencing; U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994; retrieved from http://www.ornl.gov/sci/techresources/Human—Genome/publicat/94SANTA/sequencing/chen.shtml.
Chen, C.H. Winston, et al.; Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis; Session K14—Nucleic Acids; MIXED session, Tuesday afternoon, Mar. 17, 1998, Los Angeles Convention Center; retreived from http://flux.aps.org/meetings/YR98/BAPSMAR98/abs/S2000012.html.
Chen, C.H., et al.; Laser Desorption Mass Spectrometry for high throughput DNA analysis and its applications; 1999; retrieved from http://www.osti.gov/bridge/servlets/purl/3655-nx94bv/webviewable/3655.pdf.
Chen, C.H. Winston, et al.; Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis; DOE Human Genome Program Contractor-Grentee Workshop VIII Jan. 12-16, 1999 Oakland, CA; retrieved from http://www.ornl.gov/sci/techresources/Human—Genome/publicat/99santa/45.html.
Chen, C.H. Winston, et al.; Laser mass sepctrometry for DNA sequencing, disease diagnosis, and fingerprinting; SPIE vol. 2985; 1997; pp. 70-81.
Emshwiller, E. & Doyle, J.J.; Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae). 2. Chloroplast expressed glutamine synthetase data. American Journal of Botany 89(7), 2002; pp. 1042-1056.
Emshwiller, E. & Doyle, J.J; Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae): nrDNA ITS data. American Journal of Botany 85(7); 1998; pp. 975-985.
Ecker, D.J., et al. “Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance” Proc Natl Acad Sci USA 102(22); May 2005, pp. 8012-8017.
Ecker, D.J., et al. “The Microbial Rosetta Stone Database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents” BMC Microbio15(1):19, (2005); 17 pages.
Ecker, J.A., et al. “Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry” J Clin Microbio144(8), (2006), pp. 2921-2932.
Edwards, J.R., et al; Mass-Spectrometry DNA Sequencing; Mutation Research 573 (2005) 3-12.
Edwards, J.R. et al.; DNA sequencing using biotinylated dideoxynucleotides and mass spectrometry; Nucleic Acids Research 2001, vol. 69, No. 21, e104; pp. 1-6.
Fitzgerald, M.C. et al; The Analysis of Mock DNA Sequencing Reactions Using Matrix-assisted Laser Desporption/Ionization Mass Spectrometry; Rapid Communications in Mass Spectrometry, vol. 7; 895-897 (1993).
Francisco-Ortega J., et al., Internal Transcribed Spacer Sequence Phylogeny ofCrambeL. (Brassicaceae): Molecular Data Reveal Two Old World Disjunctions; Mol Phylogenet Evol., Apr. 1999; 11(3); pp. 361-380.
Hall, T.A. et al.; Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans; Analytical Biochem. 344 (2005); pp. 53-69.
Herwig, R., et al.; Information theoretical probe selection for hybridisation experiments; vol. 16, No. 10, 2000, pp. 890-898.
Hujer, K.M. et al. “Analysis of antibiotic resistance genes in multidrug-resistant Acinetobacter sp. isolates from military and civilian patients treated at the WalterReed Army Medical Center” Antimicrob Agents Chemother 50(12), (2006), pp. 114-123.
Jacobson, K.B. et al.; Applications of mass spectrometry to DNA sequencing; GATA 8(8), 1991; pp. 223-229.
Jupe, E.R. & Zimmer, E.A.; Unmethylated regions in the intergenic spacer of maize and teosinte ribosomol RNA genes; Plant Mol Biol.; Mar. 1990;14(3); pp. 333-347.
Kirpekar, F., et al.; DNA sequence analysis my MALDI mass spectrometry; Nucleic Acids Research, 1998, vol. 26, No. 11; pp. 2554-2559.
Kim, D.H. et al.; Genetic diversity ofEchinaceaspecies based upon amplified fragment length polymorphism markers. Genome, Feb. 2004; 47(1); pp. 102-111.
Koopman, W.J.M., et al., Phylogenetic Relationships AmongLactuca(Asteraceae) Species and Related Genera Based on ITS-1 DNA Sequences; Am. J. Bot. 85(11), 1998; pp. 1517-1530.
Koster, H. et al.; A strategy for rapid and efficient DNA sequencing by mass spectrometry; Nature Biotech; vol. 14, Sep. 1996; pp. 1123-1128.
Krause, J. et al.; High Resolution Characterization of

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